Molecules & Biological Macromolecules

Question 1

What are the four types of organic molecules?

Answer 1

Carbohydrates, lipids, proteins, and nucleic acids.

Question 2

Define carbohydrate (glycan).

Answer 2

Carbohydrates are sugars that act as stores of chemical energy and as durable building materials for biological construction.

Question 3

Name each sugar with a number of carbons ranging from 3-7.

Answer 3

3. Triose
4. Tetrose
5. Pentose
6. Hexose
7. Heptose

Question 4

How does the location of the carbonyl group in a sugar molecule affect its properties?

Answer 4

If the carbonyl is located in an internal position, the molecule is a ketose (such as fructose). If it is located at one end of the sugar, then it forms an aldehyde group and the molecule is known as aldose.

Question 5

Why is the large number of hydroxyl groups in a sugar molecule important?

Answer 5

The large number of hydroxyl groups makes the sugar molecule highly soluble in water.

Question 6

Explain stereoisomerism.

Answer 6

When a carbon exists at the center of a tetrahedron, it can bond with four other molecules/atoms. Thus, though two carbon atoms may bond with the same set of four molecules, if those molecules are not placed at the same locations around the tetrahedron, the molecules are not considered to be the same; the stereoisomers will be mirror images of each other.

Question 7

What is the distinction between D and L sugars in the context of stereoisomerism?

Answer 7

It is based on the arrangement of groups attached to the asymmetric carbon atom farthest from the aldehyde. If the hydroxyl group of this carbon projects to the right, the aldose is a D-sugar; if it projects to the left, it is an L-sugar.

Question 8

Define glycosodic bonds

Answer 8

Glycosodic bonds are covalent bonds that join sugars together to form larger sugars, generating a –C–O–C– linkage between the two original molecules.

Question 9

Define disaccharides and provide two examples of them.

Answer 9

Disaccharides are molecules composed of only two sugar units. They serve primarily as fast energy stores. Examples include sucrose and lactose.

Question 10

Define oligosaccharides, discuss where they are common, and name their purposes.

Answer 10

1. Oligosaccharides are small chains of sugars.
2. They are usually found covalently attached to lipids and proteins, converting them into glycolipids and glycoproteins. They can also be found on the cell surface.
3. Because they contain so many different combinations of sugar units, these carbohydrates can play an informational role, helping the cell distinguish one cell from another and mediate specific interactions within its surroundings.

Question 11

Describe the interaction between glucose, glycogen, and the liver.

Answer 11

Liver tissue contains an insoluble polymer named glycogen. Food is transported to the liver, where it is converted to glucose and stored as glycogen. Then, as the body needs fuel, the glycogen is broken down again into glucose.

Question 12

Define starch and the two polymers that it is a mixture of.

Answer 12

Starch is a polymer of glucose found primarily in plants. Amylose (a helical molecule) and amylopectin (a branched molecule) compose starch. Starch is stored as densely packed granules, and though animals don’t synthesize starch, they can hydrolyze it.

Question 13

Define cellulose, describe its structure, and explain why animals cannot use it as food.

Answer 13

Cellulose consists of glucose monomers that form tough, durable material. Its glucose bonds are joined differently from those of other polysaccharides. Animals lack the enzyme needed to break cellulose, though it is the most abundant organic material on earth and energy-rich.

Question 14

Describe chitin.

Answer 14

Chitin is a polysaccharide made of an unbranched polymer of the sugar N-acetylglucosamine (which is similar to glucose but has an acetyl amino group instead of a hydroxyl group). Chitin is commonly found in the outer covering of insects.

Question 15

Describe glycosaminoglycans (GAGS).

Answer 15

GAGS have a sugar structure of A–B–A–B– where A and B represent two different sugars. Heparin is a common example of a GAG.

Question 16

Define lipids.

Answer 16

Lipids are a diverse group of nonpolar biological molecules whose common properties include their inability to dissolve in water, ability to dissolve in organic solvents such as chloroform or benzene. Lipids include fats, steroids, and phospholipids.

Question 17

Define fats.

Answer 17

Fats consist of a glycerol molecule linked by ester bonds to three fatty acids; the resulting molecule is called a triacylglycerol.

Question 18

Define fatty acids.

Answer 18

Fatty acids are long unbranched hydrocarbon chains with a single carboxyl group at one end. So, since the hydrocarbon end of the molecule is hydrophobic and the carboxyl group is hydrophilic, fatty acids are amphoteric.

Question 19

Explain why fatty acids are used in soap.

Answer 19

The hydrophobic end of the fatty acids can integrate itself into the grease molecule while the hydrophilic end works to break it apart.

Question 20

What is the distinction between saturated and unsaturated fatty acids?

Answer 20

Saturated fatty acids have no double bonds while unsaturated fatty acids do. The more double bonds that fatty acid chains possess, the less effectively they can be packed together. This lowers the temperature at which a fatty acid-containing lipid melts. This is why saturated fats are solids at room temperature and unsaturated fats (such as oil) are liquids.

Question 21

Define hydrogenation.

Answer 21

Hydrogenation is the process by which the double bonds of a fatty acid are reduced by hydrogen atoms. This is how margarine is formed from oil. Hydrogenation also converts some of the cis double bonds into trans double bonds, which are straight rather than kinked.

Question 22

How does the energy content of fat differ from the energy content of carbohydrates?

Answer 22

A gram of fat contains over twice the energy content of a gram of carbohydrates. The amount of carbohydrates in the body (about .5 kg) could sustain a person exerting 2000 kcal of energy for one day. In contrast, there are about 16 kg of fat equivalent to 144,000 kcal of energy.

Question 23

How are lipids stored in the body?

Answer 23

Because they are extremely insoluble in water, lipids are stored in cells in the form of dry lipid droplets. In many animals, fats are stored in adipocytes where cytoplasm is filled with one or a few large lipid droplets.

Question 24

Define steroids.

Answer 24

Steroids are built around a four-ringed hydrocarbon skeleton. One important steroid is cholesterol, which is responsible for the synthesis of several hormones such as testosterone, progesterone, and estrogen.

Question 25

Describe the structure of a phospholipid.

Answer 25

The molecule resembles a fat (triacylglycerol) but has only two fatty acid chains rather than three; it is a dicylglycerol. Phospholipids have two ends with different properties: the end with the phosphate group is hydrophilic while the end with the fatty acid tails is hydrophobic.

Question 26

Describe the functions of proteins.

Answer 26

Proteins essentially make everything happen within the cell. They can act as enzymes, as structural cables, as hormones, as membrane receptors, as transporters, as antibodies, as toxins, form blood clots, and absorb or refract light.

Question 27

How is it possible for proteins to exhibit so many functions?

Answer 27

Proteins have a diverse array of functions because they can assume virtually any molecular structure. Each protein has a unique shape and structure that allows it to interact selectively with other molecules. This trait of proteins is called specificity.

Question 28

Describe the structure of amino acids in an aqueous solution.

Answer 28

All amino acids have a carboxyl group and an amino group, separated by a single carbon atom. In an aqueous solution, the carboxyl group loses its proton and exists in a negatively charged state while the amino group accepts a proton and exists in a positively charged state. Amino acids also exhibit stereoisomerism and exist in most organisms as L-amino acids.

Question 29

Define polypeptide chain.

Answer 29

A polypeptide chain is a continuous, unbranched polymer composed of amino acids.

Question 30

How do peptide bonds form?

Answer 30

Peptide bonds are joined by the linkage of the carboxyl group of one amino acid and the amino group of its neighbor. This eliminates a molecule of water.

Question 31

What characteristic of the polypeptide gives proteins their diverse structures and functions?

Answer 31

The backbone of the polypeptide is composed of the part of the amino acid common to all of them. This is called the side chain or R group, and it is highly variable among the 20 building blocks. This variability gives proteins their diversity.

Question 32

How does the side chain or R group influence the role of the protein?

Answer 32

The side chain can exhibit a wide array of features, from being fully charged to hydrophobic, and it can participate in a wide number of covalent and noncovalent bonds. It can also act as a catalyst.

Question 33

What is the difference between intramolecular interactions and intermolecular interactions?

Answer 33

Intramolecular interactions determine the structure and activity of the molecule while intermolecular interactions determine the way in which the polypeptide interacts with other molecules.

Question 34

What are the four categories of amino acids, and how are these classifications made?

Answer 34

These classifications are based on the character of the amino acids’ side chains.

1. Polar and charged.
2. Polar and uncharged.
3. Nonpolar
4. Those with unique properties.

Question 35

Describe the polar and charged category of amino acids.

Answer 35

These four types of amino acids contain side chains that become fully charged, meaning they contain strong organic acids and bases. They are able to form ionic bonds with other charged species in the cell.

Question 36

Describe the polar and uncharged category of amino acids.

Answer 36

The side chains of these amino acids have a partial negative or positive charge and can form hydrogen bonds with other molecules. They are quite reactive.

Question 37

Describe the nonpolar category of amino acids.

Answer 37

The side chains of these amino acids are hydrophobic and unable to form electrostatic bonds with water. They vary in size and shape, allowing them to pack tightly into a particular space within the core of a protein, associating with one another as the result of van der Waals forces and hydrophobic interactions.

Question 38

Describe the properties of glycine.

Answer 38

Glycine is an amino acid that fits into the unique category. Its side chain consists of only a hydrogen atom. Because of this, glycine provides a site where the backbones of two polypeptides can approach one another very closely. It is also flexible, allowing the backbone to move or hinge.

Question 39

Describe the properties of proline.

Answer 39

Proline is an amino acid that fits into the unique category. Its side chain is hydrophobic in nature, and it can create kinks in polypeptide chains.

Question 40

Describe the properties of cysteine.

Answer 40

Cysteine is an amino acid that belongs to the unique category. Its side chain is polar and uncharged, but it has the unique property of forming a covalent bond with another cysteine to form a disulfide link.

Question 41

Define disulfide bridge.

Answer 41

A disulfide bridge forms between two cysteine amino acids that are distant from one another in the polypeptide backbone. They help stabilize the intricate shapes of the proteins.

Question 42

Define PTMs.

Answer 42

PTMs are posttranslational modifications. There are 20 basic amino acids, and though they can be altered, it must happen after their incorporation into a polypeptide chain. This is why they are called PTMs.

Question 43

Why are PTMs important?

Answer 43

PTMs can generate dramatic changes in the properties and function of a protein by modifying its three-dimensional structure, activity, life span, and interactions with other molecules. Because of PTMs, a single polypeptide can exist as a number of distinct biological molecules.

Question 44

Why is the character of an amino acid (ie, ionic, polar, or nonpolar) important in protein structure and function?

Answer 44

Most soluble proteins are constructed so that their polar residues are situated at the surface so as to associate with the surrounding water. The nonpolar resides are situated in the core of the molecule, creating a space of hydrophobia. These hydrophobic interactions inside the protein are largely responsible for protein folding and overall stability of the protein. A nonpolar environment can also enhance ionic interactions, acting as a type of catalyst.

Question 45

How can polymers be rebroken down into their monomer subunits?

Answer 45

Through hydrolysis. Hydrolysis cleaves off monomers, but it requires a special enzyme and the input of energy.

Question 46

How is glucose structured in an aqueous environment?

Answer 46

The hydroxyl group of the glucose molecule reacts with the aldehyde group, closing the monosaccharide into a ring.

Question 47

What is the distinction between alpha and beta glucose?

Answer 47

This distinction depends on the position of the hydroxyl group. If the hydroxyl group is sticking down, it is an alpha glucose molecule. If up, then beta.

Question 48

What are the five components of an amino acid?

Answer 48

1. The central carbon atom.
2. One hydrogen atom
3. One amino group
4. One carboxylic group
5. One side chain/R group

Question 49

Define Zwitterion and explain why amino acids are designated as such.

Answer 49

A Zwitterion is an ion that has both a positive and negative charge. Amino acids are designated as Zwitterions because both the a-carbonyl and a-amino groups of amino acids are ionized in aqueous solution at neutral pH, thus they have both a positive and negative charge.

Question 50

What influences the flexibility of a polypeptide chain?

Answer 50

Electron resonance in a polypeptide chain constrains peptide bonds to a plane. Single bonds of alpha carbons rotate (allowing some flexibility) which allows polypeptides to fold into higher order structures.